ISLAMABAD — Money-focused talks to repair broken U.S.-Pakistan ties and reopen NATO supply routes into Afghanistan are taking place in Islamabad this week, officials said, as Defense Secretary Leon Panetta warned Wednesday that the relationship between the two countries must be mended.

The negotiations are centered on how much the United States and other NATO countries will pay to reopen the supply route for their troops in land-locked Afghanistan, said officials on both sides, who spoke on condition of anonymity because the talks are ongoing. This week, senior Pentagon official Peter Lavoy flew to Islamabad to lead the U.S. side in talks that could lay the basis for rehabilitating ties

Speaking Wednesday during a visit to India, Pakistan’s neighbor and traditional foe, Panetta acknowledged the breakdown in trust with nuclear-armed Pakistan, which is accused by many in Washington of supporting the Taliban enemy in Afghanistan and even of giving refuge to Osama bin Laden.

“They have provided some cooperation. There are other times when frankly that cooperation is not there,” Panetta said. “But the United States cannot just walk away from that relationship. We have to continue to do what we can to try to improve (the) areas where we can find some mutual cooperation.”

However, Panetta also made two points that will be regarded as incendiary in Islamabad. He said that U.S. drone attacks against terror targets on Pakistani soil will continue, and he praised India’s role in Afghanistan – which is seen with extreme hostility in Pakistan.

Asked about the legality of drone strikes, Panetta said, “This is about our sovereignty as well.”

The relationship between Pakistan and the United States was supposed to be of strategic benefit to both sides, but since January 2011, a CIA contractor shot dead two Pakistani civilians in a street in the eastern city of Lahore; U.S. forces launched the unilateral raid on bin Laden’s compound in northern Pakistan; and, in November, U.S. aircraft accidently killed 24 Pakistani soldiers manning a checkpoint on the Afghan border.

Negotiations this week focus on how much Pakistan will charge the United States per truck that travels into Afghanistan under a new transit tax, and how much the U.S. is willing to pay to repair highways that Pakistan says have been damaged by the NATO traffic, officials said.

After the U.S.-led invasion of Afghanistan in 2001, Pakistan gave free passage to NATO supplies passing through its territory from the port of Karachi. More recently, a token $250 charge per truck was imposed. Under the new transit tax, Islamabad was initially asking for $5,250 per truck carrying a 20-foot container, and twice as much for a 40-foot container. Pakistan may be willing to settle at something close to $2,000 per truck now, officials believe.

U.S. officials are determined to keep the fee below $1,000 per truck. As an added incentive to Islamabad, Washington has offered to rebuild those torn-up highways under the U.S. civilian aid program.

A senior Senate aide said that even that fee would face opposition from some members of Congress, whose anger toward Pakistan was further inflamed by the news last month that it had jailed Shakil Afridi, the doctor who helped the CIA hunt for bin Laden, for a 33-year term.

“There is no appetite in Congress for kowtowing to these guys,” said the aide, who like other officials interviewed for this story spoke on condition of anonymity because of the sensitivity of the issue.

A Western official said that the Pakistani government also is in a quandary over how it would present any deal to a public that is rabidly anti-American. Opposition leaders, including prominent Islamists, have threatened to block the roads to NATO supply convoys should the routes be reopened.

“They have to sell it there,” said the official.

The issue of land routes to Afghanistan is taking on added significance as most coalition troops and equipment are due to be withdrawn by the end of 2014. Before Pakistan suspended use of its routes, some 30 percent of NATO supplies passed through the country, while the rest went either via air or a more time-consuming northern route via central Asia.

Earlier this week, Washington concluded a deal with three Central Asian states – Uzbekistan, Kyrgyzstan and Kazakhstan – to pull military gear out of Afghanistan, bypassing Pakistan.

A separate issue of reimbursing Pakistan’s military for money spent guarding its western border with Afghanistan, under the Coalition Support Funds program, appears to have been settled as part of the negotiations, with more than $1.1 billion to be paid to Pakistan.

It seems that Pakistan is willing for now to park two other key grievances: its opposition to U.S. drone strikes in the tribal areas and demands for a U.S. apology for the deaths of the 24 Pakistani soldiers. In retaliation for those deaths, Islamabad suspended the NATO supply routes, but by doing so it punished not only the United States but also the other 49 countries that contribute troops to the international mission in Afghanistan.

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